Run this command and it will fix your broken metadata.db automatically:
Code:
calibre-debug -c "from calibre.utils.config import prefs; import os, sqlite3; db = os.path.join(prefs['library_path'], 'metadata.db'); conn = sqlite3.connect(db); schema = conn.execute('pragma user_version=21'); conn.commit()"
Just copy paste it into a windows command prompt and press enter to run it.